iCAGES main package

Please join the iCAGES mailing list at google groups here to receive announcements on software updates.

The latest version of iCAGES (2017Jan08) can be downloaded here.

iCAGES is written in Perl and can be run as a standalone application on diverse hardware systems where standard Perl modules are installed.

Download

wget https://github.com/WGLab/icages/archive/refs/tags/v1.0.2.tar.gz

Installation

tar -zxvf icages-(version).tar.gz
mv icages-(version) icages
cd icages/
wget http://www.openbioinformatics.org/annovar/download/icages/db.tar.gz
tar -zxvf db.tar.gz

The db.tar.gz file contains resources for hg19 genome coordinate.

You can also get the file from http://www.openbioinformatics.org/annovar/download/icages/hg18_db.tar.gz and http://www.openbioinformatics.org/annovar/download/icages/hg38_db.tar.gz depending on the genome build. (Note: due to shortage of storage space, these two files are taken offline; if you need them, please contact the PI to set up a temporary link to download).

cpanm JSON
cpanm HTTP::Request
cpanm LWP
mv path-to-annovar/annovar/ ./bin/
mkdir ./bin/DGIdb
wget https://raw.github.com/genome/dgi-db/master/files/perl_example.pl -O ./bin/DGIdb/getDrugList.pl
my $output;
open (OUT, ">$output") or die "iCAGES: cannot open file $output for writing the drugs recommended for cancer driver genes\n";
'output:s'    => \$output 
print "gene_name\tdrug_name\tinteraction_type\tsource\tgene_categories\n";

into

# print "gene_name\tdrug_name\tinteraction_type\tsource\tgene_categories\n";
print "$gene_name\t$drug_name\t$interaction_type\t$source\t$gene_categories\n"; 

into

print OUT "$gene_name\t$drug_name\t$interaction_type\t$source\t$gene_categories\n"; 
print "\n" . 'Unmatched search term: ', $_->{searchTerm}, "\n";
print 'Possible suggestions: ', join(",", @{$_->{suggestions}}), "\n";

into

print OUT "\n" . 'Unmatched search term: ', $_->{searchTerm}, "\n";
print OUT 'Possible suggestions: ', join(",", @{$_->{suggestions}}), "\n";
wget http://iweb.dl.sourceforge.net/project/vcftools/vcftools_0.1.12b.tar.gz
tar -zxvf vcftools_0.1.12b.tar.gz 
mv vcftools_0.1.12b/ vcftools/
rm vcftools_0.1.12b.tar.gz
cd vcftools
make
wget https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.25.0
tar -zxvf v2.25.0.tar.gz
mv bedtools2-2.25.0 bedtools
rm v2.25.0.tar.gz
cd bedtools
make

Additional databases

Initial databases for iCAGES only includes hg19 reference genome for human. In order to annotate variants with hg18 or hg38 reference genomes, please download these additional databases compiled for these two versions of references. (Note: due to shortage of storage space, these two files are taken offline; if you need them, please contact the PI to set up a temporary link to download).

cd icages/db/
wget http://icages.wglab.org/download/icages/hg18_db.tar.gz
tar -zxvf db_hg18.tar.gz
cd icages/db/
wget http://icages.wglab.org/download/icages/hg38_db.tar.gz
tar -zxvf db_hg18.tar.gz